Transcript Welcome to the Quantitative Trait Loci (QTL) Tutorial

Welcome to the
Quantitative Trait Loci (QTL) Tutorial
This tutorial will describe how to navigate the
section of Gramene that provides information on
Quantitative Trait Loci (QTL). QTL are a statistical
creation that identifies a particular region of the
genome as containing one or more genes that are
associated with the trait being assayed or measured.
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Tutorial Tips
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Images shown may not be up to date, so
results on your searches may be different, or
the data may be displayed in a different order.
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Trait Categories in Trait Ontology
Traits at Gramene are identified by Trait Ontology (TO), and are categorized according
to:
Abiotic stress: Traits related to stresses from abiotic environment, e.g., water, light,
temperature, or chemical.
Anatomy: Traits directly measuring plant parts such as root, stem or leaf.
Biochemical: Biochemical and physiological traits, e.g., enzyme activity.
Biotic stress: Traits related to stresses from pests and pathogens.
Development: Traits related to plant and plant part development. Also includes
maturity related traits.
Quality: Traits of economic importance that may affect product quality.
Sterility or fertility: Traits related to male and female flower sterility or fertility,
including incompatibility.
Vigor: Traits related to growth and dormancy.
Yield: Traits contributing directly to yield based on economic value.
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www.gramene.org
Gramene Home Page
Click here to open QTL
Home Page
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See Navigation Tutorial for info on
navigating Gramene
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Click here for a simple
search by trait or term
(slides 6-9).
QTL Home Page
Click here to do a complex search for
multiple traits or terms (Slide 10)
Enter term for quick
search
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1. Simple Search: by Trait
Click a trait to browse
QTL in that trait category
(Slide 7)
d. Click search icon.
(Slides 8-10)
a. Search by trait name,
symbol or category,
chromosome #, QTL symbol
or accession ID. Wildcard
searches include the * (i.e.
seed*)
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b. Limit search by term
field. Default searches all
fields.
c. Limit search by
species if desired.
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Simple Search: Browse by Trait Ontology
There were 63 traits
found under the
category “Quality.”
Click on the column titles to
view a sorted display list.
B. Click to view trait summary
from the Ontology Database See
Ontology Tutorial
Click for a list of these QTL
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Number of QTL that are
detected for this trait and listed
in the QTL database
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Results for simple search
There were 4 rice QTL for “BAVEGPH”
(Basic Vegetative Phase.)
Click on the hyperlinked
column titles to sort list by that
column
Click to download tab
delimited results data
Click to go to QTL Detail
Page
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Results from all search options display this
table format
Click to view
position location on
map
Click to go to Map Set
Info (see Maps
tutorial)
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Gramene-assigned QTL
accession ID
QTL Detail
Gramene-assigned standardized trait
symbol; Click to view all QTL with this
symbol
QTL symbols and
synonyms as assigned in
the publications cited.
Linkage group (chromosome) QTL has
been mapped to; Click to view all QTL
on this chromosome
Associated data to this QTL in Gramene.
# of Associations is in parentheses. Click
on a title to open a category.
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To construct a
comprehensive query,
select criteria to include in
your search
3. Power Search
To construct a
comprehensive query,
select criteria to exclude in
your search
To select multiple trait names or
species, hold "Control" (or
"Command" on Mac) key while
selecting multiple traits.
To search rice chromosome 1, type "1*" in the "Include" field
of "Linkage Groups". With the wild card the linkage groups
with the names of "1a", "1b", and so forth, will be included.
However, it will also include other chromosomes that begin
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1, so I will type "10*", "11*" and "12*" in the "Exclude"
field of "Linkage Groups".
Click to submit (results
will appear in the format
as on slide 8.)
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QTL Help
QTL help file shows database
summary, description of terms,
and search help.
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FAQs
Search FAQ
Feedback: Submit a
question to Gramene
Click titles to expand or collapse a
question or answer
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Contact Gramene
Use the feedback button, located at the top of every page, to
provide feedback or to ask questions about Gramene.
or
Email Gramene at [email protected]
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